Throughout much of the American Southwest and mainland portions of Mexico, Woodhouse’s Scrub-Jay is a reclusive jay of the foothills and lower mountain slopes. This species resulted from a taxonomic split of the Western Scrub-Jay (Aphelocoma californica) complex that lead to recognition of the Woodhouse’s Scrub-Jay (A. woodhouseii) and California Scrub-Jay (A. californica) (Gowen et al. 2014, Chesser et al. 2016), the latter occurring in coastal states from Washington to California, south to the southern tip of Baja California.

Beyond their different geographic ranges, the Woodhouse’s Scrub-Jay occupies scrub and woodland habitats, especially pinyon–juniper (Pinus–Juniperus), where they are often inconspicuous and sparsely distributed. In contrast, the California Scrub-Jay is a bold and conspicuous species of oak woodland and scrub habitats, frequently in residential areas. Woodhouse’s Scrub-Jay differs outwardly from the California Scrub-Jay by having duller blue upperparts, grayer underparts, and a breast-band that is paler and less distinct. Relative to the latter species, the Woodhouse's Scrub-Jay has a thinner, straighter bill that is less hooked (Pitelka 1951d), which are adaptations to extract and consume pinyon pine seeds (Peterson 1993, Bardwell et al. 2001). Further, the two species exhibit differences in vocalizations (Dunn and Garrett 2001, Curry et al. 2002); the calls of Woodhouse’s Scrub-Jay are typically two-syllabled and higher pitched than the harsher, one-syllabled and lower-pitched notes of the California Scrub-Jay (Dunn and Garrett 2001).

Woodhouse’s Scrub-Jay includes seven subspecies (American Ornithologists' Union 1957) in two groups (Chesser et al. 2016), a Great Basin group and a southern Mexico group with two subspecies that are sometimes treated as a separate species (Sumichrast’s Jay) (Peterson 1992a, Peterson and Navarro-Siguenza 1999, Navarro-Sigüenza and Peterson 2004, Gowen et al. 2014). Woodhouse’s Scrub-Jay is sister to a clade that contains the California Scrub-Jay and the Island Scrub-Jay (A. insularis), endemic to Santa Cruz Island, California (Peterson 1990b, Peterson 1992a, McCormack et al. 2011). Woodhouse’s and California scrub-jays have few or no fixed differences in alleles and interbreed where their geographic ranges contact in western Nevada and east-central California, and in desert ranges of eastern California (Peterson 1990a, Peterson 1990b, Peterson 1992a). Despite this ongoing gene flow, the hybrid zone is narrow, and there is evidence for selection against hybrids (Gowen et al. 2014).

The Woodhouse’s Scrub-Jay is well known among animal behaviorists as a model subject in studies of foraging behavior and cognitive abilities, including spatial memory (Vander Wall and Balda 1981, Balda and Kamil 1989, Kamil et al. 1994, Balda et al. 1997, Bednekoff et al. 1997). Although less remarkable at storing and recovering food items than corvids, like the Clark's Nutcracker (Nucifraga columbiana), Woodhouse’s Scrub-Jay nevertheless exhibits impressive skills in locating and selecting food.

The complexity of behavioral patterns within this common and broadly distributed species continues to pose challenging questions for ornithologists. Along with its close relatives, the Woodhouse’s Scrub-Jay plays an important ongoing role in efforts to understand the ecological and evolutionary forces affecting corvids and other birds.